The occurrence and ecological impacts of emerging fungicides in the environment has gained increasing attention. This study applied an in-jar passive sampling device based on silicone rubber (SR) film to measuring the freely dissolved concentration (Cfree) of 6 current-use fungicides as a critical index of bioavailability in water and soils. The kinetics parameters including SR-water, soil-water, and organic carbon-water partition coefficients and sampling rates of the target fungicides were first attained and characterized well with their physicochemical properties. The in situ and ex situ field deployment in Hefei City provided the assessment of contaminated levels for these fungicides in rivers and soils. The Cfree of triadimefon and azoxystrobin was estimated at 0.54 ± 0.07–17.4 ± 2.5 ng L−1 in Nanfei River and Chao Lake, while triadimefon was only found in Dongpu Reservoir water with Cfree below 0.66 ± 0.04 ng L−1. The results exhibited that the equilibrium duration of 7 d was suitable for water application but a longer interval of 14 d was recommended for soil sampling. This work demonstrated the advantages of the proposed strategy in terms of fast monitoring within 2 weeks and high sensitivity down to detection limits in 0.5–5 ng L−1. The in-jar passive sampling device can be extrapolated to the evaluation for a wide coverage of organic pollutants in water and soils.