Underwater scattering caused by suspended particles in the water severely degrades signal detection performance and poses significant challenges to the problem of object detection. This paper introduces an integrated dual-function deep learning-based underwater object detection and classification and temporal signal detection algorithm using three-dimensional (3D) integral imaging (InIm) under degraded conditions. The proposed system is an efficient object classification and temporal signal detection system for degraded environments such as turbidity and partial occlusion and also provides the object range in the scene. A camera array captures the underwater objects in the scene and the temporally encoded binary signals transmitted for the purpose of communication. The network is trained using a clear underwater scene without occlusion, whereas test data is collected in turbid water with partial occlusion. Reconstructed 3D data is the input to a You Look Only Once (YOLOv4) neural network for object detection and a convolutional neural network-based bidirectional long short-term memory network (CNN-BiLSTM) is used for temporal optical signal detection. Finally, the transmitted signal is decoded. In our experiments, 3D InIm provides better image reconstruction in a degraded environment over 2D sensing-based methods. Also, reconstructed 3D images segment out the object of interest from occlusions and background which improves the detection accuracy of the network with 3D InIm. To the best of our knowledge, this is the first report that combines deep learning with 3D InIm for simultaneous and integrated underwater object detection and optical signal detection in degraded environments.