This research study is the report of an experiment conducted to find out the effects of web based inquiry science environment on cognitive outcomes in Biological science in correlation to Emotional intelligence. Web based inquiry science environment (WISE) provides a platform for creating inquiry-based science projects for students to work collaboratively using evidence and resources from the Web. All projects make use of some content from the World Wide Web, as well as additional Web pages authored for purposes of the project. This approach helps students learn to use the Internet for inquiry, critiquing Web sites, designing approaches, or comparing arguments. The term cognitive outcomes as applied to science standards for intellectual capacity attained by the students as a result or consequence of learning science. Emotional Intelligence is the silent partner of rational Intelligence — equal in importance, yet frequently overlooked and rarely schooled or tested.  In order to find out the efficacy pre test-post test non equivalent group design and static group comparison design were followed. The tools which were used in the study include the test on cognitive outcomes in Biological science and scale of Emotional intelligence. The total sample consists of 128 students. The significance of difference between means, analysis of covariance, Pearson’s product moment correlation and standard error were used for data analysis. Analysis of data showed that students intervened using web based inquiry science environment was attaining significantly higher scores than conventional group student’s cognitive outcomes. Cognitive outcomes in Biological science and Emotional intelligence were negatively correlated and web based inquiry science environment have no significant influence on enhancing Emotional intelligence.