Historical mining activities have led to the presence of enormous quantities of mining wastes, which cover large extensions of the Cartagena-La Union mining district (SE, Spain). In the present work, we study the pulse entrance of mining wastes through two temporary streams (wadis) into the Mar Menor coastal lagoon in two torrential rain events and during a dry period. The characteristics of the runoff pointed to the generation of acid mine drainages in wastes, the acidified stormwater runoff loaded with particulate and dissolved heavy metals causing toxicity in the lagoon waters. The dissolved metals, which mainly affected the sampling stations located close to the wadi discharges, were rapidly eliminated from the water column, whereas the particulate metals were transported further and affected a wider area. Finally, both particulate and dissolved metals are eliminated from the water column and are accumulated in the sediments of the lagoon. The results of the water toxicity tests using sea-urchin embryos indicated that water toxicity disappeared within a few days in the most distant stations, but lasted longer and depended on the climatic conditions of the subsequent days in stations closer to the wadi outlets.