The Mar Menor is a coastal lagoon of great socio-ecological and environmental value; in recent years, different localized episodes of hypoxia and eutrophication have modified the quality of its waters. The episodes are due to a drop in dissolved oxygen levels below 4 mg/L in some parts of the lagoon and a rise in chlorophyll a to over 1.8 mg/L. Considering that monitoring the Mar Menor and its watershed is essential to understand the environmental dynamics that cause these dramatic episodes, in recent years, efforts have focused on carrying out periodic measurements of different biophysical parameters of the water. Taking advantage of the data collected and the versatility offered by neural networks, this paper evaluates the performance of a dozen advanced neural networks oriented to time series forecasted for the estimation of dissolved oxygen and chlorophyll a parameters. The data used are obtained in the water body by means of sensors carried by a multiparameter oceanographic probe and two agro-climatic stations located near the Mar Menor. For the dissolved oxygen forecast, the models based on the Time2Vec architecture, accompanied by BiLSTM and Transformer, offer an R2 greater than 0.95. In the case of chlorophyll a, three models offer an R2 above 0.92. These metrics are corroborated by forecasting these two parameters for the first time step out of the data set used. Given the satisfactory results obtained, this work is integrated as a new biophysical parameter forecast component in the monitoring platform of the Mar Menor Observatory developed by IMIDA. The results demonstrate that it is feasible to forecast the concentration of chlorophyll a and dissolved oxygen using neural networks specialized in time series forecasts.