The net carbon uptake rate and net production rate of mycosporine‐like amino acids (MAAs) were measured in phytoplankton from 2 different melt ponds (MPs; closed and open type pond) in the western Arctic Ocean using a 13C stable isotope tracer technique. The Research Vessel Araon visited ice‐covered western‐central basins situated at 82°N and 173°E in the summer of 2012, when Arctic sea ice declined to a record minimum. The average net carbon uptake rate of the phytoplankton in polycarbonate (PC) bottles in the closed MP was 3.24 mg C · m−3 · h−1 (SD = ±1.12 mg C · m−3 · h−1), while that in the open MP was 1.3 mg C · m−3 · h−1 (SD = ±0.05 mg C · m−3 · h−1). The net production rate of total MAAs in incubated PC bottles was highest (1.44 (SD = ±0.24) ng C · L−1 · h−1) in the open MP and lowest (0.05 (SD = ±0.003) ng C · L−1 · h−1) in the closed MP. The net production rate of shinorine and palythine in incubated PC bottles at the open MP presented significantly high values 0.76 (SD = ±0.12) ng C · L−1 · h−1and 0.53 (SD = ±0.06) ng C · L−1 · h−1. Our results showed that high net production rate of MAAs in the open MP was enhanced by a combination of osmotic and UVR stress and that in situ net production rates of individual MAA can be determined using 13C tracer in MPs in Arctic sea ice.