The motivation for this study was to analyse the productivity of Taiwanese aquaculture ponds while providing recommendations for a more effective copepod harvesting. Hence, variations in copepod species composition, biomass and productivity were investigated during four separate 3 weeks of intensive sampling campaigns across an annual season. The ponds showed seasonal changes, with relatively colder water at 20 °C and lower chlorophyll-a in the winter (January 2014) compared to warm water 32 °C and higher chlorophyll-a during the long summer season (April, July, October 2013). Differences between seasons were found for phytoplankton pigments concentration in the seston. Inorganic nutrients were never limited, and the average availability of phytoplankton such as diatoms and haptophytes was sufficient to support maximal growth of zooplankton. The copepod community was characterized by low species diversity with Pseudodiaptomus annandalei and Apocyclops royi as main species. Adult copepods and copepodite stages showed total maximum biomass in October and January with 383 ± 35 μg C L− 1 and 352 ± 74 μg C L− 1, respectively, where the farmers harvesting effort was minimal. The secondary production, evaluated by the nauplii and copepodites carbon specific growth, was stable at 0.36 ± 0.10 d− 1 and 0.50 ± 0.05 d− 1, respectively. The fatty acid composition in the copepods was highly favourable during the winter campaign of which also coincided with a favourable phytoplankton composition. Lastly, this study shows evidence on the yearlong availability of copepods to the pond managers, which, based on standing stock and secondary productivity, easily could improve and intensify their harvest effort. Nauplii could be harvested all year long and adult copepods and copepodites could also be collected during the winter, allowing the pond managers to expand the sales period and thereby increase their revenue.