Urban gravel pit lake ecosystems are particularly susceptible to flooding and anthropogenic nutrient loading, and are therefore likely to be significantly affected by the future projections of precipitation extremes. Six shallow ex-gravel pit lakes at Attenborough Nature Reserve, (Nottinghamshire, U.K.), three connected to the nutrient-rich River Erewash and three isolated from it, were monitored from 2005–2008 (including the highest and 6th lowest rainfall years of a 40-year record). We aimed to compare lake ecological response to hydrological extremes and to see whether river-connected gravel pits responded differently to those fed mainly by groundwater. Our results showed that flood conditions in the river-connected lakes reduced the maximum phytoplankton biomass achieved and favoured smaller taxa (cryptophytes, Scenedesmus spp. and small centric diatoms). Consequently dissolved nitrate (NO3-N) and silica (SiO2) maxima were higher during flood years because of the reduced capacity for algal uptake, but dissolved and particulate phosphorus (P) concentrations were lower because increased flushing rates led to more effective removal of sediment-released P from the lake systems. Lakes isolated from the River Erewash responded less clearly to increased rainfall, except for a delay in the timing of the phytoplankton maximum, and a pronounced rise in SiO2 concentrations after drought conditions. Spatial comparisons also showed that nutrient pollution in the River Erewash and in storm drains feeding into one of the 'isolated' lakes (Beeston Pond) led to the existence of a turbid lake ecosystem state through the increased supply of dissolved NO3-N. The other isolated lakes had lower phytoplankton biomass and extensive aquatic plant coverage, but significantly greater proportions of bloom-forming cyanobacteria (Anabaena, Aphanizomenon), because of greater water retention times. Our results show that ex-gravel pit lakes connected to rivers may be more susceptible to ecological disruption from future flooding events and are heavily influenced by river water quality, but may be less susceptible to potentially toxic cyanobacteria blooms which may be favoured in lakes isolated from rivers with long water retention times. Artificial manipulation of urban lake hydrology to increase flushing with water of a higher quality or isolation of lakes from nutrient-rich inflows may be a useful management strategy, but the effectiveness of either approach depends on the ecological quality of the lake and inflowing river. Therefore, managing urban lakes in the face of climate change and increased urbanisation requires a detailed understanding of lake ecology and hydrology.