Although most lotic ecosystems are groundwater dependent, our knowledge on the relatively long-term ecological effects of groundwater discharge on downstream reaches remains limited. We surveyed four connected reaches of a Chinese karst stream network for 72 consecutive months, with one reach, named Hong Shi Zi (HSZ), evidently affected by groundwater. We tested whether, compared with other reaches, HSZ had (1) milder water temperature and flow regimes, and (2) weaker influences of water temperature and flow on benthic algal biomass represented by chlorophyll a (Chl. a) concentrations. We found that the maximum monthly mean water temperature in HSZ was 0.6 °C lower than of the adjacent upstream reach, and the minimum monthly mean water temperature was 1.0 °C higher than of the adjacent downstream reach. HSZ had the smallest coefficient of variation (CV) for water temperature but the largest CV for discharge. Water temperature and discharge displayed a significant 12-month periodicity in all reaches not directly groundwater influenced. Only water temperature displayed such periodicity in HSZ. Water temperature was an important predictor of temporal variation in Chl. a in all reaches, but its influence was weakest in HSZ. Our findings demonstrate that longer survey data can provide insight into groundwater–surface water interactions.