The mesozooplankton of a river tributary in Oceania is evaluated and is correlated against environmental, abiotic, and biological attributes of this lotic system. Abundance, distribution, and the diversity of mesozooplankton was studied at nine stations including one estuarine station during ten sampling campaigns from June 2004 to December 2005 along the Lanyang River, the largest river and estuarine ecosystem in northeastern Taiwan. Mesozooplankton was dominated by copepods, cladocerans, and fish larvae. Among all samples, the highest abundances of mesozooplankton (5,049.36 individuals m−3) occurred in the estuary station in August 2004, which also corresponds to the highest salinities (37.0), indicating the marine role in shaping the estuarine planktonic assemblages. The abundance of mesozooplankton and number of mesozooplankton taxa were significantly higher in samples of the estuarine station than in the riverine stations (p < 0.05, one-way ANOVA). The number of mesozooplankton taxa number was affected by water temperature (r = 0.697; p = 0.025, Pearson’s correlation) that was primarily influenced by the weather that was in turn affected by seasonal monsoons.