Based on the data from four oceanographic censuses in the Minjiang estuary and Xinghua bay during April and September 2008, this paper compared the spatial-temporal distribution of shrimp density between the two kinds of waters, involved in some impact factors such as dominant species, background of topography and geomorphy, as well as hydrological features. Results showed that total weight density (22.05kg/km²) at the Minjiang estuary was lower than that (23.33kg/km²) at the Xinghua bay, while total individual density (12.34×10³ ind./km²) at the Minjiang estuary was higher than that 8.42×10³ ind./km²) at the Xinghua bay during April. Same as in April, the total weight density (205.54kg/km²) at the Minjiang estuary was lower than that (329.60kg/km²) at the Xinghua bay, while total individual density (131.25×10³ ind./km²) at the Minjiang estuary was higher than that 95.79×10³ ind./km²) at the Xinghua bay in September. The phenomenon was related with the individual size of shrimp species from the two different waters. In the Xinghua bay, the most dominant species was a euryhaline large size species, Parapenaeopsis hardwickii, with high dominance and great contribution to total weight density, while other dominant species with low dominance and small contribution. But in the Minjiang estuary, brackish species, a very small size shrimp, Acetes chinensis were the important dominant species with the most percent in individual densities and the greatest contribution to the total individual density. The different body size of dominant species between the two waters formed because of large size Parapenaeopsis hardwickii as the main dominant species at the Xinghua bay while small size Acetes chinensis, adapted to low salinity, as the important dominant specie at the Minjiang estuary. At the Minjiang estuary, the most shrimp resource aggregated in the south area which was thought as the main fishing ground, and, September was thought as the main fishing season because both weight density and individual density in September were far higher than those in April at the Minjiang estuary. The seasonal runoff of the Minjiang River and topography of the estuary were main environmental reasons which produced the variation in the estuary. At the Xinghua bay, spawning and feeding ground of shrimps lay in waters near the mouth of the bay in September, and the wintering ground located in the deeper outside waters of the bay in winter, related with distribution of shrimp weight density. The main dominant species Parapenaeopsis hardwickii, a warm-water species occupied 89.43% of total shrimp weight density determined the distribution pattern in April. The mixture of different water masses in waters near the mouth of the bay was another reason determined the distribution pattern. The shrimp dominant species in September showed a more diversify trend than that in April both in the Xinghua bay and the Minjiang estuary, while the dominant species at the Minjiang estuary is more diversify than that at the Xinghua bay compared with the two different kind of waters.