<PAGE>   1


                                                                     EXHIBIT 4.2

                        WAIVER AND SUPPLEMENTAL AGREEMENT

         THIS WAIVER AND SUPPLEMENTAL AGREEMENT (this "Supplement") is made as
of the 13 day of April, 2000, by and between RAILAMERICA, INC., a Delaware
corporation (the "Company"), and EGS Associates, L.P., a Delaware limited
partnership, EGS Partners, L.L.C., a Delaware limited liability company, BEV
Partners, L.P., a Delaware limited partnership, Jonas Partners, L.P., a New York
limited partnership, EGS Management, L.L.C., a Delaware limited liability
company, William Ehrman, Frederic Greenberg, Jonas Gerstl and Julia Oliver
(collectively the "Shareholders").



                                    RECITALS

         WHEREAS, the Company and the Shareholders (other than EGS Management,
L.L.C. and Julia Oliver) and Frederick Ketcher, James McLaren and William
Lautman (the "Former Members") are parties to that certain Agreement, dated as
of August 21, 1998 (the "Original Agreement"), pursuant to which the Company
agreed to modify certain terms of the Company's 1998 Common Stock Purchase
Rights Agreement (the "Rights Agreement") on the condition that the
Shareholders, other than EGS Management, L.L.C. and Julia Oliver, and the Former
Members enter into the Original Agreement; and

         WHEREAS, the Company has agreed to further modify those terms of the
Rights Agreement as set forth on Exhibit A attached hereto, as well as those
terms of the Original Agreement as set forth below, on the condition that the
Shareholders enter into this Supplement;

         NOW, THEREFORE, in consideration of the premises and for other good and
valuable consideration, the receipt and sufficiency of which are hereby
acknowledged, the parties hereto agree as follows:

         1. COMPANY SECURITIES. Each of the Shareholders represents and agrees
that Schedule 1 attached hereto accurately and completely sets forth as of April
12, 2000 the number of shares of the Company's common stock, $.001 par value
(the "Common Stock"), owned of record or beneficially by any Shareholder. No
Shareholder owns of record or beneficially any other securities of the Company
not set forth on Schedule 1 for such Shareholder or any other Shareholder. Each
of the Shareholders agrees that they will not acquire beneficially or of record,
individually or in the aggregate, in excess of 25% of the outstanding shares of
Common Stock.

         2. VOTING. The Shareholders agree to vote all of their shares of Common
Stock with respect to any matter brought to a vote of the stockholders of the
Company, whether at an annual or special meeting of such stockholders or by
written consent of such stockholders either (a) in favor of (i) the nominees of
the Company's management and (ii) the proposals of the Company's management, in
either case consistent with the recommendations of the Company's management or
(b) in the same proportion as the holders of the Common Stock other than the





<PAGE>   2

Shareholders; provided, however, that the foregoing shall not modify or
eliminate the Shareholders' obligations under paragraph 3 of the Original
Agreement.

         3. REPRESENTATIONS AND WARRANTIES. In order to induce the Company to
enter into this Supplement and to amend the Rights Agreement, each of the
Shareholders represents and warrants to the Company that none of the Former
Members is either a member or an employee of any of the Shareholders or a member
of a "group" (within the meaning of Rule 13d-5 under the Securities Exchange Act
of 1934, as amended) which includes any of the Shareholders. In addition, the
Shareholders acknowledge that the United States securities laws prohibit any
person who has received material, non-public information concerning the Company
from purchasing or selling the securities of the Company or from communicating
such information to any other person under circumstances in which it is
reasonably foreseeable that such person is likely to purchase or sell securities
of the Company in reliance upon such information. The Shareholders agree not to
disclose any such non-public information in violation of the United States
securities laws.

         4. WAIVER. The Company hereby waives the provisions of Section 1 of the
Original Agreement which restrict the Shareholders and the Former Members
individually and in the aggregate from holding more than 19.9% of the
outstanding Common Stock to allow the Shareholders to hold, in the aggregate, no
more than 25.0% of the outstanding Common Stock. In the event that (i) the
Shareholders, individually or in the aggregate, acquire beneficially or of
record in excess of 25.0% of the outstanding Common Stock, (ii) the Original
Agreement is determined to be unenforceable by a court of competent jurisdiction
or (iii) the Shareholders challenge the enforceability of the Original
Agreement, the foregoing waiver shall be void and of no further force and
effect.

         5. EFFECT ON ORIGINAL AGREEMENT. Except as specifically provided
hereby, the Original Agreement is and remains unmodified and in full force and
effect and is hereby ratified and confirmed.

         6. AGREEMENTS OF ADDITIONAL SHAREHOLDERS. Each of EGS Management,
L.L.C. and Julia Oliver agrees to be bound by the terms of the Original
Agreement.

         7. GOVERNING LAW. This Supplement shall be deemed a contract made under
the laws of the State of Delaware and for all purposes shall be governed by and
construed in accordance with the laws of such State applicable to contracts made
and to be performed entirely within such State.

         8. EXECUTION IN COUNTERPARTS.This Supplement may be executed in
counterparts and all of which counterparts shall for all purposes be deemed to
be an original, and which counterparts shall constitute but one and the same
instrument.



<PAGE>   3


         IN WITNESS WHEREOF, the parties hereto have caused this Supplement to
be duly executed as of the date first above written.

                                   RAILAMERICA, INC.


                                   By: /s/ Gary O. Marino
                                      ------------------------------------------


                                   EGS ASSOCIATES, L.P., a Delaware limited
                                   partnership


                                   By: /s/ William Ehrman
                                      ------------------------------------------


                                   EGS PARTNERS, L.L.C., a Delaware limited
                                   liability company


                                   By: /s/ William Ehrman
                                      ------------------------------------------

                                   BEV PARTNERS, L.P., a Delaware limited
                                   partnership


                                   By: /s/ William Ehrman
                                      ------------------------------------------


                                   JONAS PARTNERS, L.P., a New York limited
                                   partnership


                                   By: /s/ Jonas Gerstl
                                      ------------------------------------------


                                   EGS MANAGEMENT, L.L.C., a Delaware limited
                                   liability company


                                   By: /s/ William Ehrman
                                      ------------------------------------------



<PAGE>   4



                                   /s/ William Ehrman
                                   ---------------------------------------------
                                   William Ehrman


                                   /s/ Frederic Greenberg
                                   ---------------------------------------------
                                   Frederic Greenberg


                                   /s/ Jonas Gerstl
                                   ---------------------------------------------
                                   Jonas Gerstl


                                   /s/ Julia Oliver
                                   ---------------------------------------------
                                   Julia Oliver




<PAGE>   5


Schedule 1

Below is a listing of the number of shares of the Company's common stock, $.001
par value (the "Common Stock"), owned of record or beneficially owned by each of
the below listed Shareholders as of April 12, 2000.


SHAREHOLDER                                    SHARES OF COMMON STOCK OWNED
-----------                                    ----------------------------
EGS Associates, L.P.                                     610,298
Bev Partners, L.P.                                       380,815
EGS Overseas Fund                                          6,100
EGS Partners Managed Account A                            17,567
Jonas Partners, L.P.                                      62,195
EGS Partners Managed Account B                         2,679,162
Fred Greenberg                                               100
Total                                                  3,756,237