Background: Although malaria decline has been observed in most sub-Saharan African countries, the disease still represents a significant public health burden in Tanzania. There are contradictions on the effect of ownership of at least one mosquito net at household on malaria mortality. This study presents a Bayesian modelling framework for the analysis of the effect of ownership of at least one mosquito net at household on malaria mortality with environmental factors as confounder variables. Methods: The analysis used longitudinal data collected in Rufiji and Ifakara Health Demographic Surveillance System (HDSS) sites for the period of 1999–2011 and 2002–2012, respectively. Bayesian framework modelling approach using integrated nested laplace approximation (INLA) package in R software was used. The space time models were established to assess the effect of ownership of mosquito net on malaria mortality in 58 villages in the study area. Results: The results show that an increase of 10 % in ownership of mosquito nets at village level had an average of 5.2 % decrease inall age malaria deaths (IRR = 0.948, 95 % CI = 0.917, 0.977) in Rufiji HDSS and 12.1 % decrease in all age malaria deaths (IRR = 0.879, 95 % CI = 0.806, 0.959) in Ifakara HDSS. In children under 5 years, results show an average of 5.4 % decrease of malaria deaths (IRR = 0.946, 95 % CI = 0.909, 0.982) in Rufiji HDSS and 10 % decrease of malaria deaths (IRR = 0.899, 95 % CI = 0.816, 0.995) in Ifakara HDSS. Model comparison show that model with spatial and temporal random effects was the best fitting model compared to other models without spatial and temporal, and with spatial–temporal interaction effects. Conclusion: This modelling framework is appropriate and provides useful approaches to understanding the effect of mosquito nets for targeting malaria control intervention. Furthermore, ownership of mosquito nets at household showed a significant impact on malaria mortality.