The relationship between species diversity and ecosystem functioning is one of central topics in modern ecology, but variable and controversial patterns have been found depending on ecosystem type, organism type and scale. Such patterns call for mechanistic exploration within an integrative modelling framework. Lakes, especially reservoirs, are highly disturbed ecosystems, and the relationships between species diversity and ecosystem functioning likely differ from those of terrestrial ecosystems. Disturbance can have a great impact on local diversity and resource use efficiency (RUE) of phytoplankton assemblages and thereby influence these relationships. To elucidate how disturbance influences the diversity of phytoplankton and its relationship with ecosystem functioning, we analysed datasets from two groups of waterbodies (large-sized reservoirs and small-sized reservoirs) subjected to different disturbance regimes. We also investigated the mechanisms potentially underlying the relationships using structural equation modelling. A unimodal relationship between species richness and productivity was found in large-sized reservoirs and in small-sized reservoirs in dry seasons, while a positive linear relationship was detected in small-sized reservoirs in wet seasons. Cyanobacteria dominance increased the RUE of phytoplankton and decreased its evenness more significantly in large-sized reservoirs than in small reservoirs. The effects of water temperature and resources availability (TP) on species richness also changed with disturbance regimes. Disturbance is an important factor modifying the responses of phytoplankton communities to environmental gradients, and disturbance regimes at regional scale can largely shape the relationship between phytoplankton diversity and ecosystem functioning.