Small, semi-enclosed basins have often been the location of human settlements; however, this has subjected them to extensive anthropogenic use, negatively impacting the water quality and increasing their susceptibility to eutrophication. A coupled depth-averaged hydrodynamic-biogeochemical model has been configured of the shallow, microtidal Christchurch Harbour estuary, Dorset UK, to investigate processes driving declines in ecosystem health with particular emphasis on understanding the impact of changing river flows, river nutrient inputs and solar radiation. Instances of summer oxygen undersaturation and increased levels of chlorophyll were found to coincide with regions within the estuary yielding long residence times, even under low nutrient conditions. Inverse relationships between time undersaturated and both river flow and river nutrient concentration were observed but with no significant correlation between time undersaturated and solar irradiance which we attribute to the estuary's shallow nature. Our results showed that although river flow controls estuarine renewal, river nutrient concentration plays the greatest role in driving eutrophication development in small, shallow semi-enclosed basins.