Design is the fundamental soul to all branches of engineering. It is a prime context for understanding how civil engineers use critical thinking and mathematical thinking in engineering problem-solving. However, information about the interrelation between these two types of thinking in real-world engineering practice is found lacking in the literature. This paper presents the first-hand experience of developing a substantive theory which relates both critical thinking and mathematical thinking used by practicing engineers in the civil engineering design process. The qualitative research using modified grounded theory method was employed in this study. Data were generated from semi-structured interviews with practicing engineers from two engineering consultancy firms. Six essential processes of justifying decisions reasonably in engineering design process were identified, namely complying requirements, forming conjectures, drawing reasonable conclusions, defending claims with good reasons, giving alternative ways and selecting and pursuing the right approach. Findings of this study may advise prospective civil engineers of the applicability and indispensability of critical thinking and mathematical thinking in making and justifying decisions during the engineering design process. The study also contributes useful information to engineering education on fulfilling the expectations of engineering program outcomes set by the Engineering Accreditation Council.