The Taupo Volcanic Zone (TVZ) is in the Waikato and the Bay of Plenty regions of North Island of New Zealand and contains many volcanic lakes of diverse history, physiography, and limnology. The lakes vary in size (0.2 to 620 km2), mixing regime (monomictic and polymictic), and trophic status (oligotrophic to supertrophic). The purpose of this study is to develop an understanding of the sediment-pore water interactions over a range of trophic conditions and how the biogeochemical cycles influence the lake ecosystem and the implications that this has for management of the TVZ lakes. The monthly changes in composition of lake water, pore water, sediments and stable isotopes of dinitrogen gas were monitored in five monomictic TVZ lakes (Taupo, Tarawera, Okataina, Rotoiti and Ngapouri) of widely varying trophic state, in order to evaluate the interaction between sediments and lake water. In particular, 15N enrichment in the benthic nepheloid layer (BNL), sediment-pore water geochemistry, the lead record in the sediment and silicon as a potential limiting nutrient for diatom growth were studied. In addition to the monthly analysis, discrete studies were extended to 9 other lakes of the Rotorua District (Te Arawa Lakes) to reinforce the findings of the monthly study. The applicability of the natural abundance of nitrogen gas isotope ratios was used to indicate the spatial distribution of nitrogen transformations in the water column and sediment pore waters of Lake Ngapouri. A method is introduced to extract gas from water samples to measure δ15N [N2] Samples were collected from the epilimnion, hypolimnion, benthic nepheloid layer and at 5 cm intervals from the sediment pore waters at monthly intervals for one year. Values of δ15N [N2] ranged from -1 to 0.28 ‰ in the epilimnion, -1.5 to 1.25 ‰ in the hypolimnion, -1.8 to 12.2 ‰ in the benthic nepheloid layer and -0.7 to 3.5‰ in sediment pore waters. Values of δ15N [N2] showed a strong seasonal pattern that was related to the loss of dissolved oxygen in the hypolimnion during seasonal stratification. Increases in 15N-enriched dinitrogen take place in the benthic nepheloid layer during the periods of anoxia (taken to be dissolved oxygen concentrations < 0.2 mg L-1) and may be related to abundant ammonium substrate (up to 3.6 mg L-1) to support denitrification. Nitrate concentrations increased up to 0.5 mg L-1 with increasing duration of anoxia. We hypothesise that an alternative electron acceptor besides oxygen is required to support the nitrification needed for the production of nitrate. Iron and manganese hydroxides and oxides from material sedimenting out of the water column may have induced chemo-nitrification sufficient to oxidize ammonium in the anoxic benthic nepheloid layer. The nitrate formed would mostly be rapidly denitrified so that the δ15N [N2] would continue to become enriched during the presence of anoxia, as observed in hypolimnion and benthic nepheloid layer of Lake Ngapouri. The changes in δ15N [N2] values indicate the potential use of isotope ratios to identify and quantify potential chemo-nitrification/denitrification in the water column and sediment pore waters of lakes. The study of δ15N [N2] was extended to 11 Taupo Volcanic Zone lakes in order to test the wider applicability of this method. . The stratified lakes showed enrichment of δ15N [N2] in the hypolimnion of up to 20.2‰ during stratification (autum 2007). A subset of five lakes was sampled monthly for up to one year. Water samples were taken from the epilimnion, hypolimnion and 0.1 m above the sediment-water interface (benthic boundarynepheloid layer, BNL), and from within the sediment at 5 cm depth intervals. Values of δ15N [N2] varied widely spatially and temporally. Gas extracted from the surface waters of all lakes remained close to equilibrium with the atmosphere (around 0‰). The hypolimnion showed some enrichment in autumn (up to 1.2‰), whilst samples from the BNL were strongly enriched in 15N. Maximum BNL values of 15N [N2] were 0.4‰ for Lake Taupo, 1.3‰ for Lake Tarawera, 5.3‰ for Lake Okataina, 6.4‰ in Lake Rotoiti and 12.2‰ in Lake Ngapouri. Enrichment of 15N [N2] within the BNL was greatest in lakes of highest trophic status and anoxic hypolimnia, suggesting diagenesis of particulate organic matter as the source of fractionation. Hypolimnion and BNL δ15N [N2] values correlated closely with volumetric hypolimnetic oxygen demand (VHOD) (R2 = 0.92, P <0.001) and ‘Trophic Level Index’ (TLI) as an indicator of trophic status (R2= 0.77, P <0.001). Sediment and pore water samples were collected monthly from the central basins of five monomictic Taupo Volcanic Zone lakes of varying trophic state, to examine the diagenetic processes influencing the availability of major, trace elements and nutrients. A wide range of redox, diagenetic, dissolution and precipitation processes occurred, and these were specific to the compound examined, the lake and season. The dominant process associated with the onset of anoxia involved reduction, with nitrate to ammonium, manganic to manganous, ferric reduced to ferrous and sulfate to sulfide, as organic carbon was metabolised to carbon dioxide. The products of reduction were either reprecipitated as sulfides (especially pyrite) or transported to the oxic zone and oxidised (especially Mn). Ammonium was oxidised to nitrate and in the presence of anoxic conditions was denitrified. With burial the processes of hydrolysis and hydration of the siliceous sediments (including diatoms) released silicon and aluminium to the pore waters, with the Si diffusing to the lake and Al forming colloids and clay minerals. Phosphate, arsenate and many trace heavy metals (Cu, Zn, Hg, Pb and U) were released to the pore waters as the particulates containing them were dissolved and then adsorbed onto newly formed colloids or mineral phases. Protonation of small amounts of biogenic carbonates raised the concentrations of magnesium, calcium and strontium in the near-surface pore waters. Barium appeared to be transported as barite to the sediments and released into solution once sulfate concentrations decreased under reducing conditions. Geothermal fluid inputs in lakes Tarawera (surface-water) and Rotoiti (sub-surface) were important for inputs of conservative elements (Li, B, Na and K). The pore waters showed strong seasonal changes in Fe, Mn, NH4+, SO42- and associated ions such as the phosphates (H2PO4-, HPO42- PO43-) driven mostly by changes in redox potential and the depth to which oxygen penetrated during mixed lake conditions. With hypolimnetic anoxia in lakes Okataina, Rotoiti and Ngapouri, concentrations of Fe, Mn and NH4+ increased in upper pore waters and SO42- decreased. It is likely that polyoxides (PO4 and AsO4 species) and chalcophilic elements (Cu, Zn, Pb, Hg) undergo some degree of redox cycling, either directly or indirectly in association primarily with Fe, Mn and SO42-. Average annual fluxes of nutrient species were calculated from near-surface diffusion gradients using Ficks first law. Oligotrophic lakes (Taupo, Tarawera and Okataina) typically had higher fluxes of Fe, Mn and Si from the sediment to the overlying lake water while eutrophic lakes (Rotoiti and Ngapouri) had higher fluxes of NH4+ and total dissolved P from the sediment and S and NO3- into the sediments. Geothermal fluid inputs to Lake Rotoiti had influenced conservative element concentrations, especially Na (2006 mg m-2 yr-1). The range of fluxes of nutrients in the five lakes was 16.5 to 377 mg m-2 yr-1 for NH4+, 1.3 to 110 mg m-2 yr-1 for total dissolved phosphorus and 0.05 to 18.5 mg m-2 yr-1 for reactive PO4 species. In lakes there is rapid deposition and often little bioturbation of lead, resulting in an excellent depositional history of changes in both natural and anthropogenic sources. The objective of this study was to use sediments from a regionally bounded set of lakes to provide an indication of the rates of environmental inputs of lead whilst taking into account differences of trophic state and lead exposure between lakes. Intact sediment gravity cores were collected from 13 Rotorua lakes in North Island of New Zealand between March 2006 and January 2007. Cores penetrated sediments to a depth of 16-30 cm and contained volcanic tephra from the 1886 AD Tarawera eruption. The upper depth of the Tarawera tephra enabled prescription of a date for the associated depth in the core (120 years). Each core showed a sub-surface peak in lead concentration above the Tarawera tephra which was contemporaneous with the peak use of lead alkyl as a petroleum additive in New Zealand. An 8 m piston core was taken in the largest of the lakes, Lake Rotorua, in March 2007. The lake is antipodal to the pre-industrial sources of atmospheric lead but still shows increasing lead concentrations from < 2 up to 3.5 µg g-1 between the Whakatane eruption (5530 ± 60 cal. yr BP) and the Tarawera eruption. Peaks in lead concentration in Lake Rotorua are associated with volcanic tephras, but are small compared with those arising from recent anthropogenic-derived lead deposition. These results show that diagenetic processes associated with iron, manganese and sulfate oxidation-reduction, and sulfide precipitation, act to smooth distributions of lead from anthropogenic sources in the lake sediments. The extent of this smoothing can be related to changes in sulfate availability and reduction in sulfide driven by differences in trophic status amongst the lakes. Greatest lead mobilisation occurs in mesotrophic lakes during seasonal anoxia as iron and manganese are released to the pore water, allowing upward migration of lead towards the sediment-water interface. This lead mobilisation can only occur if sulfides are not present. The sub-surface peak in lead concentrations in lake sediments ascribed to lead alkyl in petroleum persists despite the diagenetic processes acting to disperse lead within the sediments and into the overlying water. Intact sediment cores were taken from the deepest basins of nine lakes in the Taupo Volcanic Zone, New Zealand, to investigate the factors controlling silicon (Si) concentrations in sediment pore waters and the flux of Si to the overlying lake water. The lakes ranged in trophic state from oligotrophic to highly eutrophic. A Si transport model developed from the vertical gradients of pore water concentrations simulated Si gradients with high precision (r2 >0.95, p <0.01) in lakes where there were no volcanic tephra layers or significant geothermal inflows. The ubiquitous presence of diatom frustules in the sediment was likely responsible for release of silicon to the pore waters and subsequent diffusion to overlying lake waters. Fluxes of silicon were related to the trophic status of the lake and were greatest in eutrophic lakes where diatom populations reduced epilimnetic silicon concentrations to <1 mg L-1. Temporal variations in the concentrations of Si, N, and P suggest that over most of the year diatom growth in the oligotrophic lakes is limited by nitrogen, or co-limited by nitrogen and phosphorus, whilst in some eutrophic lakes silicon may limit diatom growth during mixed conditions and phosphorus and/or nitrogen may limit phytoplankton growth when the lake is stratified. The rapid decline in Si concentrations below 0.1 mg L-1 after lake mixing is likely to increase dominance of non-siliceous flagellated species and cyanobacteria over diatoms. The challenge facing lake managers is there is not one single factor that controls water quality. Biogeochemical cycles controlling the availability and cycling of nutrients cannot be separated from those processes controlling other chemical species. Conservative components are needed to compare, contrast and understand non-conservative transitions. The overall budget of the lake cannot be fully understood without including these processes. Where lead has not been significantly remobilised its peak concentration in combination with the depth to the Tarawera Tephra (a non-mobile marker) can be used to assess sedimentation rates by dating the sediments and allowing historical nutrient concentrations TVZ lakes to be derived. Understanding the lake specific sediment diagenetic processes coupled with ecological modelling should enable remediation strategies to be better targeted. The rapid depletion in silicon in some TVZ lakes suggests there is potential for the use of reactive silicon as a remediation method. δ15N [N2] extracted from the BNL or near-bottom waters may be a useful indicator of trophic state and could potentially be used as a monitoring tool to rapidly assess changes in trophic state in stratified lakes or in lakes not routinely monitored.