In the pursuit of effective scientific communication, scholars employ argumentation—an idea-anchoring process using reliable evidence. This study focuses on nurturing scientific argumentation skills among 280 high school students in the Philippines, specifically in general biology, using Toulmin’s model. Participants from Bayambang National High School responded to a 15-item open-ended questionnaire; six items were used for Toulmin’s analysis, categorizing responses into five levels. Using Chi-square tests, we explored associations between response distribution, grade levels, and gender differences. Results show a correlation between grade levels and argumentation proficiency, notably 12th-grade students in levels 4 to 5. No significant gender-based differences emerged, indicating fairness in argumentation skills. Emphasizing the positive impact of integrating argumentation and scientific literacy in fostering critical thinking, Toulmin’s model for daily science assessments is recommended. Effective teacher questioning and dilemmatic queries stimulate diverse thinking. Educators defining criteria for a “good” argument and providing targeted instruction for students’ proficiency are pivotal. Studying formative assessment in Philippine biology refines practices, informs academia, and supports an inclusive education system for educators and policymakers, recognizing the dynamic nature of argumentation skills.