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In this paper, a method for joint sea surface rainfall intensity (RI), wind speed, and wave height retrieval based on spaceborne global navigation satellite system reflectometry (GNSS-R) data is proposed, which especially considers the effects between these two parameters. A method of rainfall detection (RD) according to different wind speed ranges is also proposed by mitigating the impact of swell and wind speed. The results, with data collected over the oceans near Southeast Asia, show that the RD method has a detection accuracy of up to 81.74%. The RI retrieval accuracy can reach about 2 mm/h by simultaneously correcting the effects of wind speed and swell. The accuracy of wind speed retrieval is improved by about 5% after removing rainfall interference through RD in advance. After considering the influence of wind speed and eliminating rainfall interference, the retrieval accuracy of significant wave height (SWH) is improved by about 18%. Finally, the deep convolutional neural network (DCNN) model is built to estimate the SWH of the swell. The results show that the retrieval accuracy of the swell height is better than 0.20 m after excluding rainfall interference. The proposed joint retrieval method provides an important reference for the future acquisition of multiple high-precision marine geophysical parameters by spaceborne GNSS-R technology. [ABSTRACT FROM AUTHOR]