Understanding the factors causing a decline of water quality is important to ecologists, but particularly challenging given the complexity of natural systems. New Zealand’s freshwater ecosystems are under threat from increased eutrophication, and in the Waikato region this is intensified with the presence of common carp (Cyprinus carpio). The overall aim of this thesis was to capture the environmental and biological changes of a natural pond environment when carp were introduced at a high density, and to develop and test a DNA based approach of assessing zooplankton communities for quick and easy monitoring of lakes. The ecological aspect of this thesis explored how carp influenced the physical and chemical variables, as well as the biological communities of a shallow lake environment. Suspended sediments and nitrogen increased in the presence of carp. The zooplankton communities changed through time and were associated with small suspended sediments, but there was no observed influence on the zooplankton community driven by carp. This study illustrates how a new introduction of carp may have little impact on an already degraded system, such as those commonly seen in the Waikato region. The genetic component of this thesis aimed to determine the suitability of the 28S nuclear gene region as an ecological tool used in the routine monitoring of lakes. A reference library was created with 336 zooplankton individuals, including 60 rotifer, nine cladoceran, and seven copepod taxa. Sequence success was high (79%) and support for identification was generally high at the species level. These findings showed that the 28S region could be used to sample entire zooplankton communities taken from natural environments. Next generation sequencing was used to sequence the entire zooplankton communities and test the effectiveness of 28S to capture the abundant and less abundant taxa, and ultimately determine its use as a tool for ecologists. Samples were identified and counted prior to sequencing to validate the results. High and moderate abundant zooplankton taxa successfully generated sequences and were correctly identified but primer biases were apparent with the low abundant taxa. There was no evidence to support that metabarcoding can provide an estimation of abundance, as the number of sequences generated was correlated with body size. However, metabarcoding appears to be able to determine the trophic state of lake ecosystems based on the composition of the rotifer community. Overall findings show how adding additional stressors to an already degraded lake may not result in the predicted outcome. This shows that the work needed to restore or remediate the system is not as simple as removing the one stressor predicted to be causing the majority of issues (e.g. carp), but reducing all stressors that are associated with the degradation of the lake (e.g. nutrients, sediments). This thesis also shows the benefits of including DNA based techniques in ecological monitoring.