During its first years, MBL members raised enough funds to sustain the MBL. Although Whitman did not receive a salary, he managed the MBL funds according to his own judgment, often without waiting for permission from the trustees. Determined to deliver high quality research and teaching, Whitman appeared not to fear the possibility of a financial deficit. In 1897, to avoid possible financial difficulties, the MBL Corporation voted to put control of spending in the hands of the trustees. However, Whitman and his supporters advocated strongly for scientists to be in control.
With the mounting expenditures related to the growth of the MBL, Whitman became concerned about financial resources. Nevertheless, when in 1900 the University of Chicago offered to fund the MBL, Whitman refused. However, two years later in 1902 the Carnegie Institution also made an offer to the MBL, which Whitman could not afford to decline but was able to negotiate to some extent. As it was finally accepted, the Carnegie offer granted to the MBL $10,000 per year for three consecutive years. Before the offer was accepted as well as during the years following 1902 when the MBL actually received funding from the Carnegie Institution, Whitman constantly remarked that the independence of the MBL was sacred and that receiving the money should not imply a transfer of ownership —not even unofficially.
In a 1902 letter to Conklin, which Whitman wrote a few months before the MBL officially accepted the Carnegie offer, Whitman says: “you may see that we are well enough off without abandoning the ship to the Carnegie ownership. If you and the rest feel that, under all the circumstances my suggestion is fair, I hope you will not fail to give it as hearty support as you think it deserves.” The conversation about the Carnegie grant went on between Whitman and Conklin, and just a few months later, after the official acceptance, Whitman wrote: “The $10,000 offered us from the Carnegie Institution is indeed generous so long as it is given to support and not to own.”