Lake Kasumigaura, which is composed of the two basins (Nishiura and Kitaura), is a large, shallow, hypereutrophic lake. Phytoplankton and water quality records from the past forty years were analysed to elucidate whether or not, when, and what type of certain regime shifts may have occurred, based on using inferential regime shift detectors. Characteristics of the phytoplankton and water quality changes were similar at 6 sampling sites in the two basins, with 20 water quality parameters being classified into four groups, based on cluster analysis. Shifts in dominant plankton groups (DPGs) and water quality occurring almost concomitantly, concentration on the period from 1987 to 1992 (Shift A) and from 1997 to 2001 (Shift B), with those observed for the two basins usually being similar with small differences. Two types of inferential regime shift detectors (sequential t‐test type; Rodionov's RSD and sequential F‐test type: package strucchange in R) yielded similar timings and significances of the shifts. Furthermore, changes in skewness and conditional heteroskedasticity (package early warnings in R) usually represented early warning signals before the shifts. Correlation analysis and ratios of dissolved inorganic nitrogen (DIN) vs. total phosphorus (TP) supported the hypothesis that phosphorus was the phytoplankton biomass limiting nutrient, except for one period for the Nishiura basin. Neither the nitrogen:phosphorus (N/P) ratio hypothesis and ammonia–nitrate (NH4‐N/NO3‐N) hypothesis satisfactorily explain the DPGs before and after Shift A (Microcystis spp. and Planktothrix spp., respectively), although it may be possible that these ratios triggered the DPG change in this shift. A considerable increase in silicon was observed for Shift B when the DPGs changed from cyanobacteria to diatoms. Further studies on the accurate types and triggers of the regime shifts are necessary to better understand the interactions between ecosystem and water quality for this and similar lakes elsewhere.