Dose Monitoring of Busulfan and Combination Chemotherapy in Hodgkin or Non-Hodgkin Lymphoma Undergoing Stem Cell Transplant

Inclusion Criteria: * Patients with either Hodgkin lymphoma or non-Hodgkin lymphoma * Patients with a previously harvested hematopoietic stem cells while in complete or partial remission, or in the case of patients with stable or refractory disease are undergoing autologous transplantation because it has been recommended by their treating physician as representing their best treatment option with a goal of at minimum of 2 x 10\^6 cluster of differentiation (CD)34+ peripheral primed stem cells per kilogram of actual body weight * Cardiac ejection fraction \>= 45% or clearance by Cleveland Clinic (CCF) physician * Diffusion capacity of the lung for carbon monoxide (DLCO) of \>= 45% predicted or clearance by CCF physician * Serum creatinine \< 2.0 mg/dl * Serum bilirubin \< 2.0 mg/dl * Females of childbearing potential must have a negative pregnancy test * Patients of childbearing potential must agree to use an effective birth control method * Patient must not have any other active malignancy (or malignancy must be in remission with no evidence of disease for the past 2 years) excluding nonmelanoma skin cancer * Patients must have had at least 17 days since their most recent cytoxic chemotherapy or radiation at the time of the initiation of their preparative regimen (day -9) * Serum glutamic oxaloacetic transaminase (SGOT) \< 2 times the normal or clearance by a CCF physician * Patients who are human immunodeficiency virus (HIV) positive: * Patients must be receiving concurrent HAART therapy (highly active antiretroviral therapy) * CD4 count must be \>= 100/mm\^3 * Viral load must be =\< 10,000 copies/ml * Patients must not have concurrent opportunistic infections * There is no restriction on the number of prior chemotherapeutic regimens or radiation exposure with the exception of prior autologous or allogeneic stem cell transplantation * Eastern Cooperative Oncology Group (ECOG) performance status =\< 2 at time of consent * Subjects must have the ability to understand and the willingness to sign a written informed consent document Exclusion Criteria: * Patients who have not recovered from adverse events due to agents administered more than 4 weeks earlier OR * Prior treatment toxicities must be resolved to =\< grade 1 according to National Cancer Institute (NCI) Common Terminology Criteria for Adverse Events (CTCAE) version 4.0 * Patients with uncontrolled seizures as defined by having any seizure activity within the 3 months prior to screening * Patients who are receiving any other investigational agents * Patients with untreated brain metastases should be excluded from this clinical trial * History of allergic reactions attributed to compounds of similar chemical or biologic composition to busulfan other agents used in this study * Patients receiving any medications or substances that are inhibitors or inducers of specify cytochrome P450 (CYP450) enzyme(s) will be eligible for the study at the discretion of the consenting physician * Patients with uncontrolled intercurrent illness including, but not limited to ongoing or active infection, symptomatic congestive heart failure, unstable angina pectoris, cardiac arrhythmia, or psychiatric illness/social situations that would limit compliance with study requirements * Pregnant or breastfeeding women are excluded from this study; breastfeeding should be discontinued if the mother is treated with busulfan, cyclophosphamide, and etoposide * Patients who have had major surgical procedures or significant traumatic injury within 28 days prior to study treatment