Quantitative net sampling has been essential for zooplankton-related studies historically. However, currently, no information regarding the relationship between ocean conditions and filtering efficiency using quad-NORPAC nets is available. In this study, the influences of mesh size and ocean conditions on filtering efficiency were evaluated using data from field sampling in the Indian sector of the Southern Ocean during summer. When the impact of mesh size (63, 100, 150, and 335 µm) on filtering efficiency was assessed, the 63-µm net demonstrated the lowest efficiency, indicating that this mesh size was unsuitable for quantitatively collecting whole zooplankton during net towing. The 100- and 150-µm nets also showed lower filtering efficiencies than the 335-µm net due to clogging by phytoplankton. Moreover, excessive towing caused the overestimation of the filtering efficiency when the waves were over 2.4 m high. Thus, to collect whole zooplankton quantitatively, using nets with a mesh size of 100 µm or more is considered appropriate in the Indian sector of the Southern Ocean during summer.