The tropical monsoonal estuaries along the south-west coast of India are critical biodiversity habitats that also sustain artisanal fisheries. The key abiotic parameters that control estuarine ecosystem functioning such as salinity and sediment regimes exhibit stark seasonality driven by rivers that feed these estuaries. However, these rivers are also harnessed for hydropower generation. How the operation of these dams affects estuarine ecosystem functioning and its fisheries-based livelihoods is poorly known. In this study, we ask 1) How does hydropeaking affect estuarine salinity? 2) How is the suspended sediment delivery to the estuary modified due to reservoirs trapping sediments? 3) How do artisanal bivalve collectors in the estuary of a dammed river adapt their livelihoods in response to dam-induced changes in the estuary? We conducted this study in two free-flowing and two dammed rivers and their estuaries in Karnataka, India over a period of two years. We deployed data loggers, collected water samples and conducted interviews with bivalve collectors. We found that in the undammed rivers, estuarine salinity has a strong seasonality driven by the monsoon flood pulse and tides. In one of the dammed rivers, estuarine salinity is fully controlled by hydropeaking releases, while in the other, estuarine salinity seems unaffected by hydropeaking releases. In the undammed rivers, SSC peaks during the monsoon flooding but in the dammed rivers, SSC variability is controlled by the extent to which the flood pulse is dampened by the reservoirs. Data from the interviews suggest that bivalve availability has drastically declined in the dam-affected estuary, and bivalve collections no longer constitute a dependable source of livelihood. Former bivalve collectors now depend either on estuarine fisheries, tourism, or illicit sand mining, or they have migrated away from the estuary to find other income sources. Our study has implications for re-operating reservoirs to minimize alterations to downstream flow, sediment regimes and livelihoods.