Agricultural land use is a major source of nitrogen (N), phosphorus (P) and suspended sediment (SS) to aquatic ecosystems. Elevated inputs of N, P and SS associated with agricultural expansion and intensification have led to widespread degradation of surface waters throughout the world, causing eutrophication and excessive sedimentation of many rivers, lakes, wetlands, and estuaries. In excess, these contaminants cause diverse negative impacts on lake ecosystems such as prolific growth of phytoplankton and aquatic plants, toxic algal blooms and collapse of macrophyte beds, high turbidity and in-filling, as well as reduced biodiversity, health and resilience. Shallow peat lakes in the Waikato region of New Zealand have catchment soils that are highly erodible and readily leach nutrients, with low capacity to assimilate elevated loads of N, P and SS. These lakes have some of the poorest water quality amongst lakes in New Zealand. Constructed treatment wetlands (CTWs) are used internationally as technologies to improve the quality of stormwater and wastewater from municipal, industrial and agricultural point sources. Further, CTWs are becoming increasingly prevalent as mitigation tools to manage diffuse pollution from agricultural runoff. However, discrepancies among studies of the performance of CTWs treating diffuse sources of N, P and SS have created uncertainty for end-users. As such, more field-based research is required to establish the suitability of CTWs as management tools for diffuse agricultural runoff where flow rates are unregulated and pollutant concentrations can be highly variable. Improving our knowledge of the efficacy of CTWs within intensive agricultural landscapes will increase confidence and encourage more widespread implementation of these mitigation tools by those involved with water quality management. Actions are underway to restore several highly eutrophic Waikato peat lakes that have catchments used for intensive dairy production. Local land-care groups, landowners and lake managers are working collaboratively to improve water quality and enhance biodiversity. CTWs have been implemented as mitigation tools to manage diffuse sources of N, P and SS and reduce loads to the receiving lakes. Restoration group members additionally anticipate that CTWs will improve biodiversity through provision of supplementary habitat within the highly modified, homogeneous agricultural landscape. The primary objective of my research was to evaluate the dual benefits of CTWs as tools for nutrient and sediment attenuation, and restoration of biodiversity within peat lake ecosystems. The efficacy of CTWs treating diffuse agricultural pollution is influenced by three key elements: CTW morphology, internal contaminant cycling, and the composition of influent constituents. I quantified the magnitude, composition and variability of constituent inputs in surface waters draining small subcatchments of five shallow peat lakes. Up to 26 channelised streams were sampled seasonally over 18 months from 2010 to 2011. Subcatchments had predominantly peat, peaty loam or clay loam soil types and ranged in area from c. 1 to 195 ha (mean 23 ha; median 6 ha). Extensive spatial and temporal variation in nutrient and sediment loads was evident, driven by seasonality and differences between subcatchment soil types and farm-scale management practices. Total N concentrations were highly variable (0.24 - 13.55 mg L-1; median 2.13 mg L-1), attributable to varying concentrations of nitrate-N and particulate organic-N, which ranged from 0.01 to 10.28 mg L-1 and 0.01 to 4.63 mg L-1, respectively. Total P concentrations ranged widely (0.01 - 3.02 mg L-1; median 0.13), with exceptionally high concentrations of dissolved P in watercourses draining subcatchments with deep (≥7 m) peat soils and very low surface-water pH (< 4) (mean 1.29 mg PO4-P L-1; n=15). These results stress the importance of considering soil type when deriving appropriate environmental targets and controls for diffuse pollution from intensive agricultural peat lake catchments. Lake-catchment nutrient loads calculated from subcatchment daily loads were greater than many of those reported elsewhere in New Zealand, indicating the significance of the nutrient problem faced by water quality managers of Waikato’s shallow peat lakes. The efficacy of CTWs as management tools to attenuate diffuse sources of N, P, and SS from agricultural subcatchments of the five peat lakes was investigated concurrently. Different potential predictors of CTW performance were evaluated for up to 26 CTWs and the effect of morphological and environmental variables on internal nutrient cycling and treatment performance were elucidated. All CTWs were comprised of a sedimentation pond 'module', with around half including shallow wetland modules planted with native plant species, and three with additional sedimentation pond modules. Inflows were surface-flow watercourses diverted from modified or artificial drainage networks, and outflows were either surface-flow (through drainage channels or culverts) or filtration (through vegetated riparian margins). Morphological predictors of CTW performance included area (range 7 – 1950 m²), depth (0.2 – 2.1 m), volume (12 – 2030 m³), wetland to catchment area ratio (0.01 – 1.18), hydraulic retention time (0.2 – 37.2 h), and hydraulic loading rate (0.4 – 130 m d-1). The presence/absence of macrophytes, the outlet type and the number of CTW modules were included in analyses as categorical variables. Reductions in N, P and SS differed considerably among CTWs, driven by varying influent concentrations and dominant forms of N, P, and SS, as well as CTW morphologies and internal nutrient cycling. Generally, CTWs with larger areas and volumes had higher removal rates of nitrate, total N and coarse sediments, while deeper CTWs more effectively reduced particulate N and volatile SS. Macrophytes improved removal of nitrate and P, whereas filtration outlets frequently increased ammonium. Greater accumulated sediment depths were associated with reduced P removal efficiency, signifying the importance of CTW maintenance such as periodic removal of accumulated sediment. Increasing the number of CTW modules generally improved pollutant removal performance; thus, implementing individualised CTW treatment-train concepts is recommended. Zooplankton communities were studied to investigate the value of CTWs as tools to improve the biodiversity of peat lake ecosystems through provision of supplementary habitat. Zooplankton are an essential component of healthy functioning lake and wetland ecosystems. Despite this, zooplankton communities within CTWs in agricultural landscapes remain unstudied. Zooplankton taxa richness, total abundance and community composition were compared among three habitat types (lakes, CTWs and drainage ditches) within the five study catchments. CTWs supported zooplankton species otherwise absent from lake and drain habitats, increasing the biodiversity of the highly-modified peat lake catchments. Taxa richness of CTWs was higher than that of drains, and a few CTWs had greater diversity than some of the lakes. Zooplankton communities were significantly influenced by habitat area, depth and pH, as well as ammonium and phosphate concentrations, water temperature, dissolved oxygen, and macrophyte cover. This thesis explored opportunities for refining CTW designs, to enhance habitat diversity and support zooplankton species that improve ecosystem function and may increase CTW performance in agricultural landscapes. The results of my research present key design considerations for surface flow CTWs treating diffuse agricultural pollution from peat lake catchments used for intensive dairy production. Collectively, the findings of this thesis provide a scientific basis for more comprehensive, holistic CTW designs to mitigate inputs of N, P and SS, and quantitative evidence of the value of agricultural CTWs as water quality and restoration management tools for peat lake ecosystems. This thesis also provides recommendations for future research to improve our understanding of the complex hydrological and biogeochemical processes driving nutrient losses from peat lake catchments used for intensive dairy production, to inform restoration and rehabilitation of shallow peat lake ecosystems in New Zealand.