We studied the plankton dynamics of two semi-enclosed marine coastal inlets of the north of Jurong Island separated by a causeway (SW Singapore; May 2012-April 2013). The west side of the causeway (west station) has residence times of ca. one year and is markedly eutrophic. The east side (east station) has residence times of one month and presents lower nutrient concentrations throughout the year. The higher nutrient concentrations at the west station did not translate into significantly higher concentrations of chlorophyll a, with the exception of some peaks at the end of the South West Monsoon. Microzooplankton were more abundant at the west station. The west station exhibited more variable abundances of copepods during the year than did the east station, which showed a more stable pattern and higher diversity. Despite the higher nutrient concentrations at the west station (never limiting phytoplankton growth), the instantaneous phytoplankton growth rates there were generally lower than at the east station. The phytoplankton communities at the west station were top-down controlled, largely by microzooplankton grazing, whereas those of the east station alternated between top-down and bottom-up control, with mesozooplankton being the major grazers. Overall, the trophic transfer efficiency from nutrients to mesozooplankton in the eutrophic west station was less efficient than in the east station, but this was mostly because a poor use of inorganic nutrients by phytoplankton rather than an inefficient trophic transfer of carbon. Some hypotheses explaining this result are discussed.