Maintaining data dependability within wireless sensor network (WSN) systems has significant importance. Nevertheless, the deployment of systems in unattended and hostile areas poses a major challenge in dealing with noise. Consequently, several investigations have been conducted to address the issue of noise-affected data recovery. Nevertheless, previous research has primarily focused on the internal noise of the system. Neglecting to include external factors that impact the WSN system in the study might lead to findings that are not true to reality. Hence, this research takes into account both internal and external noise factors, such as rain, fog, or snow conditions. Moreover, in order to maintain the temporal characteristics and intersensor relationships, the data from multiple sensor nodes are consolidated into a two-dimensional matrix format. The stacked convolutional autoencoder (SCAE) model is proposed, which has the capability to extract data features. The stack design of the SCAE enables it to effectively mitigate the issue of vanishing gradients. Moreover, the weight sharing approach used between the two subnetworks also enhances the efficiency of the weight initialization procedure. Thorough experiments are conducted using both simulated WSN systems and real-world sensing data. Experimental results demonstrate that the SCAE outperforms existing methods for reconstructing noisy data.