One of the applications applied most nowadays is web based instruction (WBI). Although there are many studies on WBI, no study which researched the relations between beliefs for WBI, WBI tools acceptance levels and web pedagogical content knowledge (WPCK) of science and technology pre-service teachers was found among these studies. The aim of this study is to examine this relation. In accordance with this aim, the study group of the study consisted of 363 pre-service teachers. The data collected from pre-service teachers under the research were collected with scales of belief, tools acceptance and WPCK towards WBI. 3 scales were used for the data collection in the research. The data were analyzed with structural equation modeling in the research. As a result of the research, behavioral and contextual beliefs in WBI beliefs were medium level. Perceived usefulness, ease of use, perceived attitude and intention positively affect WBI tools acceptance levels of pre-service teachers. When the relation between beliefs, tools acceptance levels and web pedagogical content knowledge of science and technology education pre-service teachers towards WBI is analyzed, it is seen that beliefs towards WBI affect acceptance levels of WBI tools and WBI tools acceptance levels affect web pedagogical content knowledge.