The research described in this thesis was designed to yield information on the impact of particle-bound pesticides on organisms living in the interface between sediment and water column in a temporarily open estuary (TOCEs). It was hypothesized that natural variables such as salinity and temperature and anthropogenic stressors such as particle-bound pesticides contribute to the variability of the system. A multiple line of evidence approach is necessary due to the variability in sediment type, contaminant distribution and spatial and temporal variability within the ecosystem in particular within TOCEs. The first aim of this thesis was to identify which particle-bound pesticides are important to the contamination of the Lourens River estuary (Western Cape, South Africa), taking into account their environmental concentrations, physico-chemical and toxicological properties (Exposure assessment). The second aim was to identify spatial and temporal variations in particle bound pesticide contamination, natural environmental variables and benthic community structure (effect assessment). The third aim was to test the hypothesis: "does adaptation to fluctuating salinities lead to enhanced survival of the harpacticoid copepod Mesochra parva when exposed to a combination of particle associated chlorpyrifos exposure and hypo-osmotic stress during a 96 h sediment toxicity test?" The last aim was to identify the driving environmental variables (including natural and anthropogenic stressors) in a "natural" (Rooiels River) compared to a "disturbed" (Lourens River) estuary and to identify if and how these variables change the benthic community structure in both estuaries. Data produced in this research thus provide important information to understand the impact of pesticides and its interaction with natural variables in a temporarily open estuary. To summarise, this study indicated, by the use of the multi-evidence approach, that the pesticides endosulfan and chlorpyrifos posed a risk towards benthic organisms in a temporarily open estuary in particular during spring season. Furthermore an important link between pesticide exposure/ toxicity and salinity was identified, which has important implications for the management of temporarily open estuaries.