Investments are a demanding and, at the same time, threatening indicator for enterprises not only in the time of depression such as the current coronavirus pandemic but also under normal market conditions. The goal of this article is to propose a methodology for assessing financial risks and investment development. The proposed methodology integrates the use of new modern and classical economic-statistical methods, which makes it an effective tool for the sustainability of enterprises. At the same time, the methodology can be used as an auxiliary tool for enterprise management in the investment decision-making process. In the first step, a methodology was created using a commercial software tool where the pdevelopment of the cash-flow indicator and the accumulated cash flow were modeled in order to calculate the net present value (NPV). The statistical modeling was performed using the one-way analysis of variance (ANOVA). The normality was monitored using the Shapiro–Wilk test, and the Kruskal–Wallis test was chosen as the non-parametric test. The deliverable of the applied methods was the creation of a mathematical model in the form of an algorithm that is applicable in different enterprises in Slovakia.