The present study investigated the intra-ecosystem variability of nutrient enrichment (nitrogen -N- and phosphorus -P-), density of faecal coliforms (i.e., as a proxy of sanitary conditions), and ecological responses of the zooplankton community structure in a tropical urban coastal lagoon, following eutrophication, changes in rainfall, and episodic sandbar openings. Surface waters were monthly taken over 14 years (1992-2005) within the long-term monitoring program ECOlagoas from two sampling stations at the Imboassica lagoon (Northern of the Rio de Janeiro State, Brazil): near a domestic wastewater channel (SEWAGE station), and at the limit to the sea (SANDBAR station). Changes in faecal coliforms and nutrient concentration reduced water quality due to untreated sewage inputs, which was intensified by artificial sandbar openings mainly under low rainfall, such as observed in February 2001. Indeed, a greater depth and subsequent volume of water of the Imboassica lagoon during the acidification period (i.e., attributed to the increased rainfall, and lower frequency of sandbar openings) contributed to dilute the faecal coliform only in the SANDBAR station. In turn, the zooplankton community structure showed that episodic sandbar openings promoted the loss of their functional features derived from a reduction and replacement of species over time, even in the period of lower frequency of sandbar opening and dilution of nutrient concentrations. Our findings indicate that sandbar openings are not the best management practice when facing coastal eutrophication, once it may cause harmful effects on sanitary conditions and ecological community related to zooplankton, mainly in periods of decline in rainfall.