This study focused on the spatial and temporal variation of water qualities and the phytoplankton and zooplankton standing crop of southwestern Taiwan. Data were collected from 30 cruises of research and fishermen vessels between August 1999 and December 2002. The yield of sergestid shrimp in this area was also analyzed for possible relationship with physical environment. Concentrations of phosphate and ammonia in the study area were highest in autumn, while the concentration of dissolved silicon peaked in winter; In spring, the concentration of all three nutrients similarly dropped to their lowest level. Regardless of seasonal variation, the concentration of dissolved silicon positively correlated with the water depth around the year. Positive correlation was found between phosphate and river discharge rates of Kao-Ping River in autumn. Negative correlation was found in spring, summer and autumn for ammonia, negative correlation in spring and autumn for dissolved silicon, respectively. Variations of phytoplankton in seasons and locations were also studied. Chlorophyll a blooms in winter but was at lowest level in summer. Concentration of total-chlorophyll a decreased with distance from the shoreline. Concentration of total-chlorophyll a negatively correlated with the river discharge rate in summer, but was positively correlated in winter. Nanophytoplankton (< 10 £gm) appeared to be the major component of phytoplankton. High standing crop of copepods was found at regions near the Liu-Chiu Yu, the estuary of Kao-Ping River, and near the coast. Significant positive correlation between phytoplankton and Copepoda standing crop indicates possible feeding and grazing relationship between them. Changes of the concentration of chlorophyll a corresponds with relative levels of phosphate and ammonia in some seasons. The period with the highest phytoplanktonic standing crop also coincides with the high yield season of sergestid shrimp (from November to March). Variation of Copepoda standing crop does not follow seasonal changes of phytoplankton. Based on the results from General Linear Model analysis, lunar phases, river discharge rates of Kao-Ping River, and the Fishing Effort (hrs/haul-boat) have significant effects on the yield (kgs/haul-boat) of sergestid shrimp respectively. The yield of sergestid shrimp in the full moon period and the last quarter of a lunar month is higher than other periods. The occurrence of thick thermocline water layer matched with the period of high CPUE of sergestid shrimp.