The multiport diffuser effluent discharge facilities constructed beneath the coastal waters were simplified in the laboratory as twin buoyant jets in a wavy cross-flow environment. The near-field flow structure of twin jets was studied by series of experiments conducted in a physical wave–current flume. The particle image velocimetry (PIV) system was used to measure the velocity field of the jets in various cross-flow-only and wavy cross-flow environments. By means of flow visualization, the distinctive “effluent cloud” (EC) phenomenon was clearly observed and the jet penetration height was found to be notably increased compared with that of cross-flow-only environment at the downstream position. It was found that the wave-to-current velocity ratio R_wc is a very important parameter for effluent discharge. A new characteristic velocity u_ch and the corresponding characteristic length scale l_mb for twin buoyant jets in the wavy cross-flow environment were defined. Using curve-fitting, a new equation to estimate the effects of the jet-to-current velocity ratio (R_jc), wave-to-current velocity ratio (R_wc) and Strouhal number (St) on the jet trajectory were derived to enhance understanding the physical processes underpinning the rise and the dilution of buoyant jets, which is critical to the design of discharge facilities.