Water quality indicators have been tied to natural or man-made surface hydraulic connection (SHC) conditions. Among these, temporally connected lakes (TCL) are hydraulic intermediates between isolated (IL) and permanently connected lakes (PCL). Therefore, the aim of this study is to answer if water quality indicators can estimate the possible overlap between the two opposed conditions of SHC (IL and PCL) with the intermediate one (TCL) in lakes with similar modifications in the water level regulation at the basin level. Among nine water variables sampled in six lakes with the three SHC conditions mentioned, chlorophyll a (Chl-a), Secchi disk (SD), and total phosphorus (TP) were identified as quality water indicators through principal component analysis. Furthermore, said indicators were used to measure their overlap and trophic state index deviations. The Chl-a, SD, and TP values in TCL showed a 0.72 overlap of PCL and IL. TP surplus measured in all the lakes was meaningful in urbanized ILs and lessened in a rural lake (PCL6) with submerged rooted macrophytes. The estimated overlap of trophic indicators between TCL, IL, and PCL in this study must be verified at a global representative scale for predictive and preventive use in the conservation of tropical coastal plain lakes.